Molecular recognition underlies most biological processes, but it is a phenomenon which is not well understood. Recently, potential energy functions have been developed that can be used to accurately calculate the conformational energies of molecules. These conformational energy calculations can be applied to the interactions of biological macromolecules, with other molecules. By examining biomolecular complexes of lowest free energy and by determining which interactions are the critical ones in stabilizing the complex, the basis for molecular recognition can be understood. We are currently using such conformational energy calculations in studies of enzyme-substrate complexes including lysozyme and other hydrolytic enzymes.